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CHECK report for genomeIntervals on malbec2

This page was generated on 2019-10-16 11:57:16 -0400 (Wed, 16 Oct 2019).

Package 652/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genomeIntervals 1.40.0
Julien Gagneur
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/genomeIntervals
Branch: RELEASE_3_9
Last Commit: 2f4755b
Last Changed Date: 2019-05-02 11:53:11 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genomeIntervals
Version: 1.40.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:genomeIntervals.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings genomeIntervals_1.40.0.tar.gz
StartedAt: 2019-10-16 01:53:29 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:55:21 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 111.7 seconds
RetCode: 0
Status:  OK 
CheckDir: genomeIntervals.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:genomeIntervals.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings genomeIntervals_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/genomeIntervals.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genomeIntervals/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomeIntervals’ version ‘1.40.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘genomeIntervals’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
interval_complement,Genome_intervals: warning in
  factor(rep(as.character(fac.comb[, 2]), times = nrows), level =
  levels(seqnames(x))): partial argument match of 'level' to 'levels'
interval_complement,Genome_intervals_stranded: warning in
  factor(rep(names(s), times = sapply(gi.list, nrow)), level =
  levels(strand(x))): partial argument match of 'level' to 'levels'
coerce,Genome_intervals-RangedData: no visible global function
  definition for ‘na.omit’
writeGff3,data.frame: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  na.omit write.table
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘benchmarking-tests.R’
  Comparing ‘benchmarking-tests.Rout’ to ‘benchmarking-tests.Rout.save’ ...13,34d12
< 
< Attaching package: 'BiocGenerics'
< 
< The following objects are masked from 'package:parallel':
< 
<     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
<     clusterExport, clusterMap, parApply, parCapply, parLapply,
<     parLapplyLB, parRapply, parSapply, parSapplyLB
< 
< The following objects are masked from 'package:stats':
< 
<     IQR, mad, sd, var, xtabs
< 
< The following objects are masked from 'package:base':
< 
<     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
<     as.data.frame, basename, cbind, colnames, dirname, do.call,
<     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
<     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
<     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
<     tapply, union, unique, unsplit, which, which.max, which.min
< 
  Running ‘consistency-tests.R’
  Running ‘fullShow.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/genomeIntervals.Rcheck/00check.log’
for details.

Installation output

genomeIntervals.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL genomeIntervals
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘genomeIntervals’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (genomeIntervals)

Tests output

genomeIntervals.Rcheck/tests/benchmarking-tests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # benchmarking tests
> # 
> # on modifications, regenerate .Rout.save with:
> # R --vanilla <./benchmarking-tests.R >& ./benchmarking-tests.Rout.save
> # and use svn' diff to check for differences
> #
> # Author: julien.gagneur
> ###############################################################################
> 
> library(genomeIntervals)
Loading required package: intervals
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

> source("fullShow.R")
> options(warn = -1)
> 
> #---------------
> # make data
> #---------------
> # toy examples
> data("gen_ints")
> 
> # non-stranded versions
> i0 = as(i, "Genome_intervals")
> j0 = as(j, "Genome_intervals")
> k0 = as(k, "Genome_intervals")
> 
> # empty intervals
> e = k[1:3,]
> e[,2] = e[,1]
> closed(e) = FALSE
> 
> #---------------
> # checks
> #---------------
> # distance to nearest
> cat("distance_to_nearest\n")
distance_to_nearest
> print( distance_to_nearest(i,j) )		# x
[1]  0  2  3  0  0  0 NA
> print( distance_to_nearest(j,i) )		# x
[1]  0  2 NA  0  0
> print( distance_to_nearest(i,k) )		# x
[1] 0.0 1.5 2.5 0.5 0.0 0.0  NA
> print( distance_to_nearest(i,e) )		# x
[1] NA NA NA NA NA NA NA
> print( distance_to_nearest(e,i) )		# x
[1] NA NA NA
> 
> print( distance_to_nearest(i0,j0) )		# x
[1]  0  0  1  0  0  0 NA
> print( distance_to_nearest(j0,i0) )		# x
[1] 0 2 0 0 0
> cat("\n")

> 
> # interval overlap
> cat("interval_overlap\n")
interval_overlap
> print( interval_overlap(i,k) )			# x
[[1]]
[1] 1

[[2]]
integer(0)

[[3]]
integer(0)

[[4]]
integer(0)

[[5]]
[1] 5

[[6]]
[1] 4

[[7]]
integer(0)

> print( interval_overlap(i,e) )			# x
[[1]]
integer(0)

[[2]]
integer(0)

[[3]]
integer(0)

[[4]]
integer(0)

[[5]]
integer(0)

[[6]]
integer(0)

[[7]]
integer(0)

> print( interval_overlap(i0,j0) )		# x
[[1]]
[1] 1

[[2]]
[1] 3

[[3]]
integer(0)

[[4]]
[1] 5

[[5]]
[1] 5

[[6]]
[1] 4 5

[[7]]
integer(0)

> cat("\n")

> 
> 
> # set operations
> cat("interval_union\n")
interval_union
> fullShow( close_intervals( interval_union(i) ) )		# x
Object of class Genome_intervals_stranded
4 base intervals and 0 inter-base intervals(*):
chr01 + [1, 4] 
chr02 + [4, 12] 
chr03 + [2, 5] 
chr02 - [5, 11] 
annotation:
  seq_name inter_base strand
1    chr01      FALSE      +
2    chr02      FALSE      +
3    chr03      FALSE      +
4    chr02      FALSE      -
> fullShow( close_intervals( interval_union(i,k) ) )		# x
Object of class Genome_intervals_stranded
6 base intervals and 2 inter-base intervals(*):
chr01 + [1, 4] 
chr01 + [6, 10] 
chr01 + [1, 1] *
chr02 + [4, 15] 
chr03 + [2, 5] 
chr01 - [4, 5] 
chr02 - [5, 11] 
chr02 - [8, 8] *
annotation:
  seq_name inter_base strand
1    chr01      FALSE      +
2    chr01      FALSE      +
3    chr01       TRUE      +
4    chr02      FALSE      +
5    chr03      FALSE      +
6    chr01      FALSE      -
7    chr02      FALSE      -
8    chr02       TRUE      -
> fullShow( close_intervals( interval_union(i0,k0) ) )	# x
Object of class Genome_intervals
3 base intervals and 2 inter-base intervals(*):
chr01 [1, 10] 
chr01 [1, 1] *
chr02 [4, 15] 
chr02 [8, 8] *
chr03 [2, 5] 
annotation:
  inter_base seq_name
1      FALSE    chr01
2       TRUE    chr01
3      FALSE    chr02
4       TRUE    chr02
5      FALSE    chr03
> fullShow( close_intervals( interval_union(e) ) )		# x
Object of class Genome_intervals_stranded
0 base intervals and 0 inter-base intervals(*):

annotation:
[1] seq_name   inter_base strand    
<0 rows> (or 0-length row.names)
> cat("\n")

> 
> cat("interval_intersection\n")
interval_intersection
> fullShow( close_intervals( interval_intersection(i,j) ) ) # x
Object of class Genome_intervals_stranded
3 base intervals and 0 inter-base intervals(*):
chr01 + [1, 1] 
chr02 - [8, 8] 
chr02 + [12, 12] 
annotation:
  inter_base seq_name strand
1      FALSE    chr01      +
2      FALSE    chr02      -
3      FALSE    chr02      +
> fullShow( close_intervals( interval_intersection(i,k) ) ) # x
Object of class Genome_intervals_stranded
1 base interval and 0 inter-base intervals(*):
chr02 + [12, 12] 
annotation:
  inter_base seq_name strand
1      FALSE    chr02      +
> fullShow( close_intervals( interval_intersection(i,e) ) ) # x
Object of class Genome_intervals_stranded
0 base intervals and 0 inter-base intervals(*):

annotation:
[1] inter_base seq_name   strand    
<0 rows> (or 0-length row.names)
> cat("\n")

> 
> cat("interval_complement\n")
interval_complement
> fullShow( close_intervals( interval_complement(j) ) )	# x
Object of class Genome_intervals_stranded
9 base intervals and 0 inter-base intervals(*):
chr01 + [-Inf, 0] 
chr01 + [2, 5] 
chr01 + [11, Inf] 
chr02 + [-Inf, 11] 
chr02 + [16, Inf] 
chr01 - [-Inf, 3] 
chr01 - [6, Inf] 
chr02 - [-Inf, 7] 
chr02 - [9, Inf] 
annotation:
  seq_name inter_base strand
1    chr01      FALSE      +
2    chr01      FALSE      +
3    chr01      FALSE      +
4    chr02      FALSE      +
5    chr02      FALSE      +
6    chr01      FALSE      -
7    chr01      FALSE      -
8    chr02      FALSE      -
9    chr02      FALSE      -
> fullShow( close_intervals( interval_complement(j0) ) )	# x
Object of class Genome_intervals
6 base intervals and 0 inter-base intervals(*):
chr01 [-Inf, 0] 
chr01 [2, 3] 
chr01 [11, Inf] 
chr02 [-Inf, 7] 
chr02 [9, 11] 
chr02 [16, Inf] 
annotation:
  inter_base seq_name
1      FALSE    chr01
2      FALSE    chr01
3      FALSE    chr01
4      FALSE    chr02
5      FALSE    chr02
6      FALSE    chr02
> fullShow( close_intervals( interval_complement(k) ) ) # x
Object of class Genome_intervals_stranded
7 base intervals and 6 inter-base intervals(*):
chr01 + [-Inf, 5] 
chr01 + [11, Inf] 
chr01 + [-Inf, 0] *
chr01 + [2, Inf] *
chr02 + [-Inf, 11] 
chr02 + [16, Inf] 
chr02 + [-Inf, Inf] *
chr01 - [-Inf, 3] 
chr01 - [6, Inf] 
chr01 - [-Inf, Inf] *
chr02 - [-Inf, Inf] 
chr02 - [-Inf, 7] *
chr02 - [9, Inf] *
annotation:
   seq_name inter_base strand
1     chr01      FALSE      +
2     chr01      FALSE      +
3     chr01       TRUE      +
4     chr01       TRUE      +
5     chr02      FALSE      +
6     chr02      FALSE      +
7     chr02       TRUE      +
8     chr01      FALSE      -
9     chr01      FALSE      -
10    chr01       TRUE      -
11    chr02      FALSE      -
12    chr02       TRUE      -
13    chr02       TRUE      -
> fullShow( close_intervals( interval_complement(e) ) ) # x
Object of class Genome_intervals_stranded
4 base intervals and 2 inter-base intervals(*):
chr01 + [-Inf, Inf] 
chr01 + [-Inf, Inf] *
chr02 + [-Inf, Inf] 
chr02 + [-Inf, Inf] *
chr01 - [-Inf, Inf] 
chr02 - [-Inf, Inf] 
annotation:
  seq_name inter_base strand
1    chr01      FALSE      +
2    chr01       TRUE      +
3    chr02      FALSE      +
4    chr02       TRUE      +
5    chr01      FALSE      -
6    chr02      FALSE      -
> cat("\n")

> 
> 
> proc.time()
   user  system elapsed 
  6.125   0.139   6.249

genomeIntervals.Rcheck/tests/benchmarking-tests.Rout.save


R version 2.12.1 (2010-12-16)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # benchmarking tests
> # 
> # on modifications, regenerate .Rout.save with:
> # R --vanilla <./benchmarking-tests.R >& ./benchmarking-tests.Rout.save
> # and use svn' diff to check for differences
> #
> # Author: julien.gagneur
> ###############################################################################
> 
> library(genomeIntervals)
Loading required package: intervals
> source("fullShow.R")
> options(warn = -1)
> 
> #---------------
> # make data
> #---------------
> # toy examples
> data("gen_ints")
> 
> # non-stranded versions
> i0 = as(i, "Genome_intervals")
> j0 = as(j, "Genome_intervals")
> k0 = as(k, "Genome_intervals")
> 
> # empty intervals
> e = k[1:3,]
> e[,2] = e[,1]
> closed(e) = FALSE
> 
> #---------------
> # checks
> #---------------
> # distance to nearest
> cat("distance_to_nearest\n")
distance_to_nearest
> print( distance_to_nearest(i,j) )		# x
[1]  0  2  3  0  0  0 NA
> print( distance_to_nearest(j,i) )		# x
[1]  0  2 NA  0  0
> print( distance_to_nearest(i,k) )		# x
[1] 0.0 1.5 2.5 0.5 0.0 0.0  NA
> print( distance_to_nearest(i,e) )		# x
[1] NA NA NA NA NA NA NA
> print( distance_to_nearest(e,i) )		# x
[1] NA NA NA
> 
> print( distance_to_nearest(i0,j0) )		# x
[1]  0  0  1  0  0  0 NA
> print( distance_to_nearest(j0,i0) )		# x
[1] 0 2 0 0 0
> cat("\n")

> 
> # interval overlap
> cat("interval_overlap\n")
interval_overlap
> print( interval_overlap(i,k) )			# x
[[1]]
[1] 1

[[2]]
integer(0)

[[3]]
integer(0)

[[4]]
integer(0)

[[5]]
[1] 5

[[6]]
[1] 4

[[7]]
integer(0)

> print( interval_overlap(i,e) )			# x
[[1]]
integer(0)

[[2]]
integer(0)

[[3]]
integer(0)

[[4]]
integer(0)

[[5]]
integer(0)

[[6]]
integer(0)

[[7]]
integer(0)

> print( interval_overlap(i0,j0) )		# x
[[1]]
[1] 1

[[2]]
[1] 3

[[3]]
integer(0)

[[4]]
[1] 5

[[5]]
[1] 5

[[6]]
[1] 4 5

[[7]]
integer(0)

> cat("\n")

> 
> 
> # set operations
> cat("interval_union\n")
interval_union
> fullShow( close_intervals( interval_union(i) ) )		# x
Object of class Genome_intervals_stranded
4 base intervals and 0 inter-base intervals(*):
chr01 + [1, 4] 
chr02 + [4, 12] 
chr03 + [2, 5] 
chr02 - [5, 11] 
annotation:
  seq_name inter_base strand
1    chr01      FALSE      +
2    chr02      FALSE      +
3    chr03      FALSE      +
4    chr02      FALSE      -
> fullShow( close_intervals( interval_union(i,k) ) )		# x
Object of class Genome_intervals_stranded
6 base intervals and 2 inter-base intervals(*):
chr01 + [1, 4] 
chr01 + [6, 10] 
chr01 + [1, 1] *
chr02 + [4, 15] 
chr03 + [2, 5] 
chr01 - [4, 5] 
chr02 - [5, 11] 
chr02 - [8, 8] *
annotation:
  seq_name inter_base strand
1    chr01      FALSE      +
2    chr01      FALSE      +
3    chr01       TRUE      +
4    chr02      FALSE      +
5    chr03      FALSE      +
6    chr01      FALSE      -
7    chr02      FALSE      -
8    chr02       TRUE      -
> fullShow( close_intervals( interval_union(i0,k0) ) )	# x
Object of class Genome_intervals
3 base intervals and 2 inter-base intervals(*):
chr01 [1, 10] 
chr01 [1, 1] *
chr02 [4, 15] 
chr02 [8, 8] *
chr03 [2, 5] 
annotation:
  inter_base seq_name
1      FALSE    chr01
2       TRUE    chr01
3      FALSE    chr02
4       TRUE    chr02
5      FALSE    chr03
> fullShow( close_intervals( interval_union(e) ) )		# x
Object of class Genome_intervals_stranded
0 base intervals and 0 inter-base intervals(*):

annotation:
[1] seq_name   inter_base strand    
<0 rows> (or 0-length row.names)
> cat("\n")

> 
> cat("interval_intersection\n")
interval_intersection
> fullShow( close_intervals( interval_intersection(i,j) ) ) # x
Object of class Genome_intervals_stranded
3 base intervals and 0 inter-base intervals(*):
chr01 + [1, 1] 
chr02 - [8, 8] 
chr02 + [12, 12] 
annotation:
  inter_base seq_name strand
1      FALSE    chr01      +
2      FALSE    chr02      -
3      FALSE    chr02      +
> fullShow( close_intervals( interval_intersection(i,k) ) ) # x
Object of class Genome_intervals_stranded
1 base interval and 0 inter-base intervals(*):
chr02 + [12, 12] 
annotation:
  inter_base seq_name strand
1      FALSE    chr02      +
> fullShow( close_intervals( interval_intersection(i,e) ) ) # x
Object of class Genome_intervals_stranded
0 base intervals and 0 inter-base intervals(*):

annotation:
[1] inter_base seq_name   strand    
<0 rows> (or 0-length row.names)
> cat("\n")

> 
> cat("interval_complement\n")
interval_complement
> fullShow( close_intervals( interval_complement(j) ) )	# x
Object of class Genome_intervals_stranded
9 base intervals and 0 inter-base intervals(*):
chr01 + [-Inf, 0] 
chr01 + [2, 5] 
chr01 + [11, Inf] 
chr02 + [-Inf, 11] 
chr02 + [16, Inf] 
chr01 - [-Inf, 3] 
chr01 - [6, Inf] 
chr02 - [-Inf, 7] 
chr02 - [9, Inf] 
annotation:
  seq_name inter_base strand
1    chr01      FALSE      +
2    chr01      FALSE      +
3    chr01      FALSE      +
4    chr02      FALSE      +
5    chr02      FALSE      +
6    chr01      FALSE      -
7    chr01      FALSE      -
8    chr02      FALSE      -
9    chr02      FALSE      -
> fullShow( close_intervals( interval_complement(j0) ) )	# x
Object of class Genome_intervals
6 base intervals and 0 inter-base intervals(*):
chr01 [-Inf, 0] 
chr01 [2, 3] 
chr01 [11, Inf] 
chr02 [-Inf, 7] 
chr02 [9, 11] 
chr02 [16, Inf] 
annotation:
  inter_base seq_name
1      FALSE    chr01
2      FALSE    chr01
3      FALSE    chr01
4      FALSE    chr02
5      FALSE    chr02
6      FALSE    chr02
> fullShow( close_intervals( interval_complement(k) ) ) # x
Object of class Genome_intervals_stranded
7 base intervals and 6 inter-base intervals(*):
chr01 + [-Inf, 5] 
chr01 + [11, Inf] 
chr01 + [-Inf, 0] *
chr01 + [2, Inf] *
chr02 + [-Inf, 11] 
chr02 + [16, Inf] 
chr02 + [-Inf, Inf] *
chr01 - [-Inf, 3] 
chr01 - [6, Inf] 
chr01 - [-Inf, Inf] *
chr02 - [-Inf, Inf] 
chr02 - [-Inf, 7] *
chr02 - [9, Inf] *
annotation:
   seq_name inter_base strand
1     chr01      FALSE      +
2     chr01      FALSE      +
3     chr01       TRUE      +
4     chr01       TRUE      +
5     chr02      FALSE      +
6     chr02      FALSE      +
7     chr02       TRUE      +
8     chr01      FALSE      -
9     chr01      FALSE      -
10    chr01       TRUE      -
11    chr02      FALSE      -
12    chr02       TRUE      -
13    chr02       TRUE      -
> fullShow( close_intervals( interval_complement(e) ) ) # x
Object of class Genome_intervals_stranded
4 base intervals and 2 inter-base intervals(*):
chr01 + [-Inf, Inf] 
chr01 + [-Inf, Inf] *
chr02 + [-Inf, Inf] 
chr02 + [-Inf, Inf] *
chr01 - [-Inf, Inf] 
chr02 - [-Inf, Inf] 
annotation:
  seq_name inter_base strand
1    chr01      FALSE      +
2    chr01       TRUE      +
3    chr02      FALSE      +
4    chr02       TRUE      +
5    chr01      FALSE      -
6    chr02      FALSE      -
> cat("\n")

> 
>

genomeIntervals.Rcheck/tests/consistency-tests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # consistency test
> #
> # Author: julien.gagneur
> ###############################################################################
> 
> 
> library( genomeIntervals )
Loading required package: intervals
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

> 
> options(warn = -1)
> 
> #---------
> # settings
> #---------
> # size of random objects
> n = 1e+3
> # chrom length
> l = 1e+3
> # nb of chroms
> k = 3
> 
> #---------
> # data generation
> #---------
> 
> randGenint = function(n,l,k){
+     m = matrix( sample(l, 2*n, replace=TRUE), nc = 2 )
+     m = cbind( apply( m, 1, min), apply( m, 1, max ) )
+ 
+     cl = matrix( sample( c(FALSE,TRUE), 2*n, replace =TRUE), nc=2 )
+     new(
+         "Genome_intervals_stranded",
+         m,
+         closed = cl,
+         annotation = data.frame(
+                 seq_name = paste("chr", sample(k, n, replace=TRUE) ),
+                 inter_base = sample( c(FALSE,TRUE), n, replace =TRUE),
+                 strand = sample(c("-", "+"), n, replace =TRUE)
+         )
+     )
+ }
> 
> i = randGenint(n,l,k)
> j = randGenint(n,l,k)
> i0 = as(i, "Genome_intervals")
> j0 = as(j, "Genome_intervals")
> 
> #---------
> # checks
> #---------
> 
> # distances from i to j
> dn = distance_to_nearest(i,j)
> 
> # distance is NA or >=0
> if( any( !is.na(dn) & dn < 0) ) stop("negative distance.")
> 
> # distance == 0 if and only if the interval overlaps another one:
> io = interval_overlap(i,j)
> if( any( ( sapply(io, length) >0 )  != (!is.na(dn) & dn ==0) ) )
+     stop("The property 'distance == 0 if and only if the interval overlaps another one' is not followed for at least one instance.")
> 
> # same test for not stranded objects
> dn0 = distance_to_nearest(i0,j0)
> if( any( !is.na(dn0) & dn0 < 0) ) stop("negative distance.")
> 
> io = interval_overlap(i0,j0)
> if( any( ( sapply(io, length) >0 )  != (!is.na(dn0) & dn0 ==0) ) )
+     stop("The property 'distance == 0 if and only if the interval overlaps another one' is not followed for at least one instance.")
> 
> # unstranded distance <= stranded distance
> delta = dn - dn0
> if( any(!is.na(delta)  & delta < 0) ) stop("some unstranded distance larger than a stranded one.")
> 
> # intersection with complement is empty
> stopifnot( nrow( interval_intersection(i, interval_complement(i) ) ) == 0 )
> 
> # distance of union with complement is 1
> # test must be done for not inter-base (or inter-base) independently
> a = interval_union(i[!inter_base(i),] )
> b = interval_complement(i[!inter_base(i),])
> 
> if(!(all.equal( distance_to_nearest( a, b ), rep(1, nrow(a) )  ) ) )
+     stop("distance of union with complement is not 1.")
> 
> # width is reported consistently
> # they should all be 4 in length (we alternate the open/closed state of the intervals
> # pairwise)
> gi <- GenomeIntervals(start=c(6,6,5,5),
+                       end=c(10,9,10,9),
+                       chromosome=rep("chr1",4),
+                       leftOpen = c(FALSE,FALSE,TRUE,TRUE),
+                       rightOpen=c(TRUE,FALSE,TRUE,FALSE))
> 
> stopifnot(all(width(gi)==4))
> 
> proc.time()
   user  system elapsed 
  5.921   0.199   6.106

genomeIntervals.Rcheck/tests/fullShow.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # the fullShow methods is a show method for Genome_intervals objects.
> # It is called by test scripts so that the full output of the tests can be checked.  
> # 
> # Author: gagneur
> ###############################################################################
> 
> fullShow <- function(object ) {
+ 	cat(
+ 			"Object of class ",
+ 			class( object ),
+ 			"\n",
+ 			sum( !inter_base(object) ),
+ 			" base interval",
+ 			ifelse( sum( !inter_base(object) ) == 1, "", "s" ),
+ 			" and ",
+ 			sum( inter_base(object) ),
+ 			" inter-base interval",
+ 			ifelse( sum( inter_base(object) ) == 1, "", "s" ),
+ 			"(*)",
+ 			":\n",
+ 			sep = ""
+ 	)
+ 	ints <- as( object, "character")
+ 	if ( !is.null( rownames( object ) ) ) {
+ 		fmt <- sprintf( "%%%is", max( nchar( rownames( object ) ) ) )
+ 		ints <- paste( sprintf( fmt, rownames( object ) ), ints )
+ 	}
+ 	cat( ints, sep = "\n" )
+ 	cat( "annotation:\n")
+ 	show( annotation(object) )
+ }
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
  0.239   0.027   0.252

Example timings

genomeIntervals.Rcheck/genomeIntervals-Ex.timings

nameusersystemelapsed
GenomeIntervals-constructor0.0700.0110.083
Genome_intervals-class0.0330.0040.037
Genome_intervals-coercion-methods000
Genome_intervals-ordering0.0540.0000.054
Genome_intervals_stranded-class0.0520.0000.051
c.Genome_intervals0.0830.0080.090
core_annotated0.0760.0080.084
distance_to_nearest-methods0.3330.0040.337
genomeIntervals-readGff31.3160.1351.472
getGffAttribute0.0740.0000.073
interval_overlap-methods0.1310.0000.132
interval_set_operations-methods0.7650.0010.766
parseGffAttributes0.0630.0010.064